FINAL WORD
Dear Epic
This problem occurs when a user created widget has a named slot and that named slot is child of a scroll box. After you use that user created widget in somewhere else and add a user created child widget to that named slot the problem occurs.
In my case:
I had a BP_MainMenu, BP_Options, BP_TabScrollTop. BP_TabScrollTop had a named slot that was the child of a scroll box(Once this is done, even if you get rid of the scroll box the problem continues).
After this I added BP_TabScrollTop to BP_Options and BP_Options to BP_MainMenu. When clicked options button, BP_Options would become visible(everything is fine at this point). Then add any user created widget inside the named slot of BP_TabScrollTop which is added to BP_Options. Again things will work just fine. But when you close and reopen unreal, BP_Options widget will no longer be visible, not just that, it will get destroyed only to leave behind its reference(Please look at the pics I provided at first message).
Here I added the specific UI that caused me all this problem. Try it out in a new project to confirm this problem.
As to why this happens, I am not sure, to me it seems like a limitation of named slot added together with a scroll box causes problems.
I hope this will be reported by an epic staff. I am willing to give any information necessery. Thanks in advance.